References for Alignment

Hi, 

I'm using the "Alignment" class in chemaxon.marvin.alignment.

I don't really understand which mode is set for the default value in running the alignent. Are  the two molecules alignmed according to the same atoms or extended atom types?

So I would like to learn more the detail of how the algorithm runs.

Is there any reference available that I can refer to ?

Thank you very much!

Best,

Flora

 

Hi,

the alignment module will go beta testing phase in April 2011. We are now currently working on documentation / user manuals. If you are interested you can be a beta tester. Although I think you already are.

The default constructor  Alignment aa = new Alignment(); launches with the GAUSS_FAST_EXTENDED_ATOMTYPE enum constant of the AlginmentProperties .This usually gives reasonable alignments in reasonable times.

The alignment can be tested in commandline with the screen3D command of jchem. The only help currently available is accessible by launching this script without parameters.

There is also a alignment GUI prototype with java webstart here:

http://prefect.chemaxon.hu/shared/akalaszi/alignment/

Hope this helps.

Regards,

Adrian

adrian wrote:

Hi, the alignment module will go beta testing phase in April 2011. We are now currently working on documentation / user manuals. If you are interested you can be a beta tester. Although I think you already are. The default constructor  Alignment aa = new Alignment(); launches with the GAUSS_FAST_EXTENDED_ATOMTYPE enum constant of the AlginmentProperties .This usually gives reasonable alignments in reasonable times. The alignment can be tested in commandline with the screen3D command of jchem. The only help currently available is accessible by launching this script without parameters. There is also a alignment GUI prototype with java webstart here: http://prefect.chemaxon.hu/shared/akalaszi/alignment/ Hope this helps. Regards, Adrian

Hi, 

I'm using the commandline with the screen3D command of jchem (as following ). I found one of the default format of the output is *.mrv.  I'm wondering if we could select the format of the output file, since I would like to  get  *.mol2 directly if possible.

Thank you very much!

SCREEN:

=======

 screen3d s -t [target molecules binary file] -q [query molecule binary file] [-a shape or match] [-c comment]

Hi Flora,

you may think of the result of the alignment written to the *_aligned.mrv file. Currently this format is hardwired to the code, but fourtunately it is easy to give a command line parameter for file type selection. I will do it soon. For the time being you can use the link above for the gui. There you can save result in any format.

I will let you know here if ready.

Cheers,

Adrian

Hi Flora, 

the feature to be able to write other than mrv files will come out in the next release 5.5 during this April.

Cheers,

Adrian